<span style="font-size: 10pt;">Etiologic Risk Group (see link below): Unknown</span>
<span style="font-size: 10pt;">*/Disease Information (sort of like the Intro to your Mini Research Write up):Buruli Ulcer is caused by the protozoan //Mycobacterium ulcerans// in which the flesh is destroyed in patches of the body. Transmission method is currently unknown as it is found primarily in neglected populations. It is present in every habitable continent, but is only highly prevalent in underdeveloped tropical regions.</span>
<span style="font-size: 10pt;">Link to TDR Targets page (if present):None</span>
<span style="font-size: 10pt;">Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)</span>
<span style="font-size: 10pt;">Essentiality of this protein: Essential in other mycobaterium</span>
<span style="font-size: 10pt;"> Is it a monomer or multimer as biological unit? (make prediction at </span><span style="font-size: 10pt;">[[@http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html]]</span><span style="font-size: 10pt;">):</span>
<span style="font-size: 10pt;">Complex of proteins?:Single protein</span>
<span style="font-size: 10pt;">Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):</span><span style="font-size: 10pt;">[[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5091859/]]</span>
<span style="font-size: 10pt;">Lysyl tRNA synthetase is druggable in worm parasites by affecting the single protein.</span>
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*EC#:
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<span style="font-size: 10pt;">Link to BRENDA EC# page: </span>
<span style="font-size: 10pt;">[[https://www.brenda-enzymes.org/enzyme.php?ecno=6.1.1.6]]</span>
<span style="font-size: 10pt;">Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):</span>
<span style="font-size: 10pt;">-- link to Sigma (or other company) page for assay (see Sigma links below)</span>
<span style="font-size: 10pt;">-- -or link (or citation) to paper that contains assay https://www.sciencedirect.com/science/article/pii/030090849290158B?via%3Dihubinformationhttps://www.sciencedirect.com/science/article/pii/030090849290158B?via%3Dihub</span>
<span style="font-size: 10pt;">-- links to assay reagents (substrates) pages.http://www.bio-rad.com/en-us/sku/5000006-bio-rad-protein-assay-dye-reagent-concentrate-450-ml?ID=5000006</span>
<span style="font-size: 10pt;">--- List cost and quantity of substrate reagents, supplier, and catalog #$129.00 for Bio-Rad Protein Assay Reagent, 450 ml #5000006</span>
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Structure (PDB or Homology model)
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<span style="font-size: 10pt;"> -- PDB # or closest PDB entry if using homology model:</span>
<span style="font-size: 10pt;"> -- For Homology Model option:</span>
<span style="font-size: 10pt;"> ---- Show pairwise alignment of your BLASTP search in NCBI against the PDB</span>
<span style="font-size: 10pt;">Image of protein (PyMol with features delineated and shown separately): [[image:https://vdsstream.wikispaces.com/site/embedthumbnail/placeholder?w=624&h=468 width="624" height="468"]]</span>
<span style="font-size: 10pt;">*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): MAHHHHHHMSSAESNIPEQFRIRRDKRARLLAEGYDPYPVAIERTHTLAEIRATYADLPTDSATEDIVGVAGRVVFARNT</span>
<span style="font-size: 10pt;">GKLCFATLQDGDGTQLQAMISLDEVGRESLDRWKADVDIGDVVYVHGTVISSRRGELSVLADSWRMAAKALRPLPVAHKE</span>
<span style="font-size: 10pt;">MSEESRVRQRYVDLIVRPQAREVARQRIAVIRAVRNALERRGFLEVETPMLQTLAGGAAARPFVTHSNALDIDLYLRIAP</span>
<span style="font-size: 10pt;">ELFLKRCIVGGFDRVFELNRVFRNEGSDSTHSPEFSMLETYQTYGTYDDSALITRELIQEVADEAIGTRQLSMPDGSVYD</span>
<span style="font-size: 10pt;">IDGEWATMEMYSSLSEALGEQITPETTVARLRDIASGLDVEIDNSVFGHGKLVEELWEHAVGNKLTAPTFVKDFPVETTP</span>
<span style="font-size: 10pt;">LTRQHRSIPGVTEKWDLYVRGVELATGYSELNDPVVQRDRFADQARAAAAGDDEAMQLDEDFLTALEYGMPPCTGTGMGI</span>
<span style="font-size: 10pt;">DRLLMCLTGLSIRETVLFPIVRPHSN</span>
<span style="font-size: 10pt;">*length of your protein in Amino Acids</span>
<span style="font-size: 10pt;">506</span>
<span style="font-size: 10pt;">Molecular Weight of your protein in kiloDaltons using the [[http://expasy.org/tools/protparam.html|Expasy ProtParam]] website</span>
56511.80
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Molar Extinction coefficient of your protein at 280 nm wavelength:<span style="color: #626262;"> 48360</span>
<span style="font-size: 10pt;">*GC% Content for gene:58.717435</span>
<span style="font-size: 10pt;">*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):>lcl|ORF1</span>
<span style="font-size: 10pt;">MISLDEVGRESLDRWKADVDIGDVVYVHGTVISSRRGELSVLADSWRMAA</span>
<span style="font-size: 10pt;">KALRPLPVAHKEMSEESRVRQRYVDLIVRPQAREVARQRIAVIRAVRNAL</span>
<span style="font-size: 10pt;">ERRGFLEVETPMLQTLAGGAAARPFVTHSNALDIDLYLRIAPELFLKRCI</span>
<span style="font-size: 10pt;">VGGFDRVFELNRVFRNEGSDSTHSPEFSMLETYQTYGTYDDSALITRELI</span>
<span style="font-size: 10pt;">QEVADEAIGTRQLSMPDGSVYDIDGEWATMEMYSSLSEALGEQITPETTV</span>
<span style="font-size: 10pt;">ARLRDIASGLDVEIDNSVFGHGKLVEELWEHAVGNKLTAPTFVKDFPVET</span>
<span style="font-size: 10pt;">TPLTRQHRSIPGVTEKWDLYVRGVELATGYSELNDPVVQRDRFADQARAA</span>
<span style="font-size: 10pt;">AAGDDEAMQLDEDFLTALEYGMPPCTGTGMGIDRLLMCLTGLSIRETVLF</span>
<span style="font-size: 10pt;">PIVRPHSN</span>
<span style="font-size: 10pt;">*GC% Content for gene (codon optimized):58.717435</span>
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Do Not Need this info for Spring (but still copy these lines to your Target page for now)
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<span style="font-size: 10pt;">Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):</span>
<span style="font-size: 10pt;">(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)</span>
<span style="font-size: 10pt;"> -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.</span>
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Primer design results for 'tail' primers (this is just 2 sequences):
CAGAGGGGTATGACCCCTATCCGGTAGCCATCGAACGCACTCACACGTTGGCCGAGATTCGTGCCACCTA
TGCCGACCTACCGACAGATTCGGCGACCGAGGACATCGTCGGTGTCGCGGGTCGAGTGGTCTTCGCGCGT
AACACCGGGAAACTGTGTTTTGCGACACTGCAGGACGGCGACGGCACCCAGCTGCAGGCGATGATCAGCC
TCGACGAGGTGGGCCGCGAATCACTGGACAGGTGGAAGGCCGACGTCGACATCGGTGACGTCGTCTACGT
GCACGGCACCGTGATCAGCTCCCGTCGGGGCGAACTATCGGTGCTCGCCGATTCCTGGCGGATGGCTGCC
AAGGCCTTGCGGCCGCTGCCGGTCGCACACAAGGAGATGAGCGAGGAGTCGCGGGTTCGTCAGCGCTACG
TCGATTTGATCGTGCGTCCACAGGCGCGGGAGGTCGCGCGACAGCGGATTGCGGTAATCCGTGCGGTGCG
TAATGCGCTGGAGCGGCGCGGGTTTCTCGAAGTCGAAACGCCAATGTTGCAGACCTTGGCCGGCGGCGCT
GCGGCGCGGCCGTTCGTCACCCATTCCAATGCCCTCGACATCGATCTTTACCTGCGTATCGCGCCGGAAC
TGTTCCTCAAGCGTTGCATCGTGGGCGGTTTCGACAGGGTCTTTGAACTAAATCGGGTGTTCCGAAACGA
AGGGTCTGATTCCACCCATTCCCCGGAATTCTCCATGCTGGAGACGTATCAGACCTATGGAACCTATGAC
GATTCGGCCCTGATCACCAGAGAGCTTATTCAAGAAGTTGCTGACGAGGCGATCGGAACCAGACAACTCT
CGATGCCTGACGGCAGCGTGTACGACATCGACGGAGAATGGGCAACTATGGAGATGTATTCCTCCTTGTC
GGAGGCACTGGGGGAACAGATCACGCCAGAGACGACGGTTGCTCGCTTACGTGACATCGCAAGCGGACTT
GACGTAGAGATTGACAACAGTGTTTTTGGTCACGGCAAACTTGTCGAGGAACTCTGGGAACATGCTGTCG
GCAACAAGTTGACGGCGCCCACATTTGTCAAGGATTTCCCAGTCGAGACAACGCCATTGACTCGTCAGCA
CCGCAGTATCCCCGGAGTAACCGAGAAGTGGGATCTCTACGTGCGCGGAGTCGAACTGGCTACCGGGTAC
TCGGAATTAAACGATCCCGTCGTCCAGCGGGACAGATTCGCTGATCAGGCCCGTGCGGCGGCCGCGGGTG
ACGACGAGGCGATGCAACTTGACGAAGATTTTCTGACGGCTCTGGAGTACGGGATGCCCCCGTGTACTGG
AACTGGAATGGGCATCGATCGGTTGTTGATGTGTTTGACCGGACTGTCAATTAGGGAGACAGTTTTGTTC
CCGATTGTTCGCCCTCACTCCAACTGA
BRENDA Link:
https://www.brenda-enzymes.org/enzyme.php?ecno=6.1.1.6
*Target (protein/gene name): Lysyl-tRNA Synthetase
*EC#:
Structure (PDB or Homology model)
Current Inhibitors: None for mycobacterium
56511.80
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for 'tail' primers (this is just 2 sequences):